Hello everyone, I tried to map Electrostatic Potential (ESP) onto the molecular surface in ChimeraX v1.0 and PyMOL v2.1, but I found that the results were very different in these two programs. Therefore, I wrote to Elaine Meng and Tom Goddard for help. For your reference, I repost the ideals of our emails below. I first calculated the ESP with DelPhi v5.1 (a relatively old version) to get the .phi file (ESP). PyMOL commands for displaying ESP on the molecular surface are as follows: ------------------------------------------------ load 1ubq.pdb bg_color white remove resn hoh remove hydrogens hide line select heavy, name c*+o*+s*+n* show surface load 1ubq.phi, e_map ramp_new e_lvl, e_map, [-7, 0, 7] set surface_color, e_lvl, 1ubq set light_count, 1 set ambient, 0.5 set reflect, 0.2 ------------------------------------------------ ChimeraX commands for displaying ESP on the molecular surface are as follows: ------------------------------------------------ open 1ubq.pdb open 1ubq.phi hide #2 set bg white surface #1 color electrostatic #1 map #2 palette -7,red:0,white:7,blue material dull lighting simple ------------------------------------------------ In PyMOL, the colors (red/blue) are mainly on the residue (E/D, K/R) tips, while in ChimeraX, the colors are spread. Besides, the surface shapes are also slightly different in these two programs. See the image (left and middle panels) for the different colors and shapes. The color difference is caused by the color offset. The shape difference is also explained below. I changed the color offset to 0. Now the color looks similar in these two programs (left and right panels). The color offset (1.4 A) in ChimeraX gives a better idea of the possible charge interactions with other molecules. ------------------------------------------------ color electrostatic #1 map #2 palette -7,red:0,white:7,blue offset 0.0 ------------------------------------------------ The summary of the explanations from Tom: ------------------------------------------------ One idea I have for why PyMol shows redder tips is because ChimeraX is showing the potential 1.4 Angstroms away from the surface since that is about how far away a binding molecule would be. PyMol may be showing the ESP values exactly on the surface. You can try using 0 offset instead of 1.4 with the "color electrostatic" command "offset" parameter. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#map ------------------------------------------------ The summary of the explanations from Elaine: ------------------------------------------------ As Tom mentioned, the rationale for the 1.4 A projection is that Chimera and ChimeraX show the solvent-excluded surface (SES), as opposed to the solvent-accessible surface (SAS). The SAS is approximately half a probe radius outward, and the SAS represents the closest possible approach of atomic centers of waters or ligands interacting with the protein, so the result is coloring by what values of the electrostatic potential (ESP) that such ligands would "see". The diagram in this page shows the relationships among SES, SAS, and probe. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> Possible reasons for difference in Pymol, if the ESP map itself is identical: (1) coloring by offset values or not. It has been my general understanding that when programs color the SES by ESP, the default approach is to color by the values one surface-probe radius outward. (2) shape/location of the surface. Is it an SES or SAS, or neither? Pymol surfaces often look more "melty" or smoothed to me than the SES in Chimera/ChimeraX. (3) the exact color-mapping, i.e. which colors at which values. Pymol ESP coloring often uses a duller-looking blue. ------------------------------------------------ All the best, Steve -- Steve Chou
